Genomic analysis shows humans evolved with few sweeping changes

Contrary to current models, humans don't seem to have undergone many selective …

Humans and chimpanzees split around five million years ago. Ever since then, we (and they) have changed a bit to adapt to the different environments we invaded and created, and the "classic selective sweep" model was widely thought to account for these changes at the molecular level. In this scenario, a new, strongly beneficial mutation increases in frequency so rapidly that it "sweeps" away all other variants at that gene and nearby sites.

Yet it is difficult to detect the evidence of such sweeps in genomic data. After analyzing 179 human genomes, an international team of researchers have concluded that these sweeps were much rarer than previously thought, and were therefore probably not a huge influence on human adaptation over the past 250,000 years. Their work is reported in Science.

Sweeps were thought to be common for two reasons. First, genetic diversity is low around regions encoding human-specific amino acid substitutions and noncoding regulatory sites, which are presumed to be important in adaptation. And second, regions of low recombination—where the rarity of exchanges between chromosomes ensures that a single sweep would cover a larger span—do in fact have lower diversity than regions of higher recombination.

Statistical analyses based on the sweeps model have identified 2000 genes as potential sites of selection, and have suggested that the genetic diversity in as much as ten percent of the human genome can be attributed to recent sweeps. But there are other explanations for these patterns of genetic variation, which can be due to many modes of natural selection, as well as demographic factors. And there are only a few known, functionally characterized instances of genetic adaptation in humans.

To assess the role sweeps have had in shaping human genetic diversity, Hernandez et al. looked at 179 genomes collected as part of the 1000 Genomes Project. These represent four distinct populations: Utah residents with northern and western European ancestry; Japanese from Tokyo; Han Chinese in Beijing; and Yoruba from Ibidan, Nigeria. The three populations with Eurasian ancestry are thought to have split from the Yoruba more than 100,000 years ago and from each other about 23,000 years ago, so any sweeps would cause extreme differences in alleles between the populations.

They found that, in contrast to predictions of the sweep model, lows in diversity around human-specific changes that affect protein sequences are the same depth as those around synonymous substitutions, those in which the DNA changes that do not cause changes in a protein. In addition, genetic regions coding for proteins and noncoding regulatory regions are not very different among the four populations. They conclude that few human-specific amino acid changes, and therefore little of human evolution, resulted from classic sweeps.

This is the scientific method at its best. The classic sweep model seemed consistent with the available data until the recent technological advances allowed the sequencing of many human genomes. The authors used this new information to reveal the inadequacies of the current model, and note that new tests must be devised to detect the actual genetic mechanisms that drove human adaptation. They suggest that Genome Wide Association studies should be immensely useful in this regard.

This is the scientific method at its best. The classic sweep model seemed consistent with the available data until the recent technological advances allowed the sequencing of many human genomes. The authors used this new information to reveal the inadequacies of the current model, and note that new tests must be devised to detect the actual genetic mechanisms that drove human adaptation. They suggest that Genome Wide Association studies should be immensely useful in this regard.

It's finds like these that are most fascinating, specifically because of what you’ve said here in your last paragraph.

It’s too bad that some folks may read about this and twist it to fit their worldview, proclaiming that science doesn’t know what it’s doing – just look at how it changes on a dime – and such..

The reality is that statistical studies rarely if ever represent science at its best. The wannabe scientists involved are usually working with over simplified models and statistical data that has no prospect of discriminating between different models with reasonably complex assumptions. In fact, usually the scientists even if they are pretty good ones have not even managed to think of anything more than an unreasonably over simplified model. In this case, it looks like the scientists may have reasonable evidence that a stupid model was in fact wrong. That is something. But, it is not much of a contribution to understanding anything that is right.

It is entirely possible humans did not arise from selective pressure at all. Maybe the genes that make us more "us" than other species were not the result of some evolutionary pressure but random. It is possible the change merely put us in a category where we did not have much competition. So the change, which is always random, just put us in a whole new category not more adaptive to certain pressures.

This would help me, at least, to understand why we humans have so many characteristics that don't seem to fit into an "evolutionary advantage" unlike other species. I can understand the ability to have language as an advantage but I see no evolutionary pressure to refine our language skills to the state that they are presently.The same goes for Art, Science, etc. Oh, but having big brains was an evolutionary advantage it has been argued. Really? All I could see evolution giving us is the smarts to be "smart enough". I know this is a subjective thing, what is smart enough? What I see as I look at other species is just being a little smarter is good enough, so why the gift to us, or curse depending on how one views it heh, to be so much smarter?

As I look at modern humans, compared to other species, we are not just given gifts to survive but to really thrive and change the whole nature of the game. What other animal has basically eliminated selective pressures from their species? Humans basically have. Sorry to get all philosophical, but humans have always seemed like they don't really fit the refinement through evolutionary pressure model as well as they should heh.

The reality is that statistical studies rarely if ever represent science at its best. The wannabe scientists involved are usually working with over simplified models and statistical data that has no prospect of discriminating between different models with reasonably complex assumptions. In fact, usually the scientists even if they are pretty good ones have not even managed to think of anything more than an unreasonably over simplified model. In this case, it looks like the scientists may have reasonable evidence that a stupid model was in fact wrong. That is something. But, it is not much of a contribution to understanding anything that is right.

Well, we've seen expressions of our underlying selves in activities we do in real life. I could see some scientists sitting in a room, staring out a window thinking "notice how when cars became relevent, horses and buggies just disappeared. I wonder if the same happened to some of our genetics?"

But since genetics changes so slowly over time, I find it hard to imagine a sweeping event that derives from our genetics and not from, say, a natural catastrophe wiping out a population only leaving select genetics around.

Darn. I was hoping that this study had actual paleo-DNA from peat bog bodies. But the data was just modern sequences made by the 1000 Genomes Project.

The research was all done with database queries and extrapolated backwards to common ancestors. I really can't get excited about speculative data mining, especially when the result is merely ... evolutionary (rather than revolutionary).

As a non-biologist, I found this article a little challenging to read. If I understand the article correctly, in the last 250k yrs, few new genes have emerged that "sweep" away all competing variations, which was an unexpected finding for them. Correct me if I'm wrong, but don't we typically expect about 1 change per 100k yrs (rough order of magnitude)? So 250k yrs would only allow for 1-5 changes in the genome. So how do you get 2000 sites of selection? This is orders of magnitude above what I would expect.

More importantly, what qualifies as "human genome" in this study? Are they focusing on specific types of genes, sequences, strips of DNA, chromosome groupings, mitochondiral DNA, ... etc? I'd like to know more about their measurement techniques.

Finally, I find some of the early posters' remarks to be trollish, and reflect more on the posters' ideas/personality/lack thereof, than on the nature of any given field of study.

"In science, 'fact' can only mean 'confirmed to such a degree that it would be perverse to withhold provisional assent.' I suppose that apples might start to rise tomorrow, but the possibility does not merit equal time in physics classrooms."

The reality is that statistical studies rarely if ever represent science at its best. The wannabe scientists involved are usually working with over simplified models and statistical data that has no prospect of discriminating between different models with reasonably complex assumptions. In fact, usually the scientists even if they are pretty good ones have not even managed to think of anything more than an unreasonably over simplified model. In this case, it looks like the scientists may have reasonable evidence that a stupid model was in fact wrong. That is something. But, it is not much of a contribution to understanding anything that is right.

It's kind of confusing what this is aimed at given that the study summarized here is the one using statistical analysis.

As a non-biologist, I found this article a little challenging to read. If I understand the article correctly, in the last 250k yrs, few new genes have emerged that "sweep" away all competing variations, which was an unexpected finding for them. Correct me if I'm wrong, but don't we typically expect about 1 change per 100k yrs (rough order of magnitude)? So 250k yrs would only allow for 1-5 changes in the genome. So how do you get 2000 sites of selection? This is orders of magnitude above what I would expect.

I'm not a biologist, but I think you're conflating the # of sweeps with sites of selection on which they may act. The latter is only a list of things they're focusing the tests on, not the quantifiable number of changes at them over time.

As I look at modern humans, compared to other species, we are not just given gifts to survive but to really thrive and change the whole nature of the game. What other animal has basically eliminated selective pressures from their species? Humans basically have. Sorry to get all philosophical, but humans have always seemed like they don't really fit the refinement through evolutionary pressure model as well as they should heh.

Human survival in so many novel situations, e.g., Siberia, with the same bodies we would use near the Equator, is based on the ability to adapt using technology. Try passing on the instructions for how to prepare food, build structures, manufacture tools and weapons, and make clothing without our massively evolved cerebral cortex, and perhaps you'll start to see the selective pressures.

This research shows that genetic sweeps didn't happen after the human species came into existence. It says nothing about genetic sweeps that happened before this. After all, all humans, no matter which ethnic group they belong to, are fully human, and thus descended from the tiny group of humans in Africa who were the result of the last speciation event in the human lineage.

Like a lot of science, this shouldn't be taken at face value - it is the result of looking at the problem with one particular, and very limited, methodology (looking for the keys under the lamppost, because the light is better there). In this case, they looked only at single-nucleotide changes, because the sequencing method could detect those. Unfortunately, it is becoming increasingly clear that many important differences between humans and chimps (for instance) are caused by other sorts of mutations, such as insertions, deletions, rearrangements, and copy-number variations. The technique they used (low-coverage short-read sequencing) can not see those changes. So they frequently saw evidence of sweeps around areas that did not have any of the changes that they were looking for (e.g., SNPs that changed an amino acid). Then they used that fact to argue that there is some sort of mysterious force causing what appear to be sweeps in lots of places, so any evidence of sweeps around their favored types of changes must not be real. They aren't necessarily wrong, but there is a very good possibility that there were in fact a lot of sweeps, with many of them caused by mutations that they could not see.

BTW,other recent reports about human genetics and evolution are rather likely to be wrong for the same reason or similar reasons, including reports that many Europeans and Asians carry genes from Neanderthals. I just recently got back from the big Genomics meeting (AGBT) and lots of the senior people were talking privately about how junky these sorts of analyses are.

This is not meant as a slam - this is how science works. You draw the best conclusions you can from the best data you have, and then wait until better data either confirms or refutes your hypothesis.

Mandatory flame war starting comment: See its not evolution... its God.

Now discuss...

I like to think it's both.

Why?

Possibly because, from a completely logical perspective, the lack of an irrefutable argument for the existence of God is not proof of non-existence. People are as myopic about evolution disproving God as some Christians (no, not remotely all) are about disproving evolution. Both sides fail to understand the other's arguments and then derive conclusions based on the caricature.

It may surprise you to learn that there are Christian churches that teach God as one who works within the laws of the universe instead of vice versa. And such a God is capable of using existing universal forces to organize planets, arrange for life on those planets, and even create a nearly infinite variety of formations in said universe. It may even surprise you further to discover that such a God is not only well within the teachings of the Bible, but has a rather compelling fit with everything we understand about The Way Things Are both scientifically and spiritually.

In any case, attempting to explain away God via evolution is a waste of time since the only thing you can do via evolution is prove that a particular church's teachings are incorrect. And even then, there are undoubtedly further refinements to evolution that will surprise us and may open up possibilities that neither side had considered before.

People that think the book is closed on the subject simply do not fully understand the subject. Which is the same ignorance accusation that armchair scientists throw at the caricature of religious people.

Mandatory flame war starting comment: See its not evolution... its God.

Now discuss...

I like to think it's both.

Why?

Possibly because, from a completely logical perspective, the lack of an irrefutable argument for the existence of God is not proof of non-existence. People are as myopic about evolution disproving God as some Christians (no, not remotely all) are about disproving evolution. Both sides fail to understand the other's arguments and then derive conclusions based on the caricature.

It may surprise you to learn that there are Christian churches that teach God as one who works within the laws of the universe instead of vice versa. And such a God is capable of using existing universal forces to organize planets, arrange for life on those planets, and even create a nearly infinite variety of formations in said universe. It may even surprise you further to discover that such a God is not only well within the teachings of the Bible, but has a rather compelling fit with everything we understand about The Way Things Are both scientifically and spiritually.

In any case, attempting to explain away God via evolution is a waste of time since the only thing you can do via evolution is prove that a particular church's teachings are incorrect. And even then, there are undoubtedly further refinements to evolution that will surprise us and may open up possibilities that neither side had considered before.

People that think the book is closed on the subject simply do not fully understand the subject. Which is the same ignorance accusation that armchair scientists throw at the caricature of religious people.

Mandatory flame war starting comment: See its not evolution... its God.

Now discuss...

I like to think it's both.

Why?

Possibly because, from a completely logical perspective, the lack of an irrefutable argument for the existence of God is not proof of non-existence. People are as myopic about evolution disproving God as some Christians (no, not remotely all) are about disproving evolution. Both sides fail to understand the other's arguments and then derive conclusions based on the caricature.

It may surprise you to learn that there are Christian churches that teach God as one who works within the laws of the universe instead of vice versa. And such a God is capable of using existing universal forces to organize planets, arrange for life on those planets, and even create a nearly infinite variety of formations in said universe. It may even surprise you further to discover that such a God is not only well within the teachings of the Bible, but has a rather compelling fit with everything we understand about The Way Things Are both scientifically and spiritually.

In any case, attempting to explain away God via evolution is a waste of time since the only thing you can do via evolution is prove that a particular church's teachings are incorrect. And even then, there are undoubtedly further refinements to evolution that will surprise us and may open up possibilities that neither side had considered before.

People that think the book is closed on the subject simply do not fully understand the subject. Which is the same ignorance accusation that armchair scientists throw at the caricature of religious people.

Possibly because, from a completely logical perspective, the lack of an irrefutable argument for the existence of God is not proof of non-existence. People are as myopic about evolution disproving God as some Christians (no, not remotely all) are about disproving evolution. Both sides fail to understand the other's arguments and then derive conclusions based on the caricature.

It may surprise you to learn that there are Christian churches that teach God as one who works within the laws of the universe instead of vice versa. And such a God is capable of using existing universal forces to organize planets, arrange for life on those planets, and even create a nearly infinite variety of formations in said universe. It may even surprise you further to discover that such a God is not only well within the teachings of the Bible, but has a rather compelling fit with everything we understand about The Way Things Are both scientifically and spiritually.

In any case, attempting to explain away God via evolution is a waste of time since the only thing you can do via evolution is prove that a particular church's teachings are incorrect. And even then, there are undoubtedly further refinements to evolution that will surprise us and may open up possibilities that neither side had considered before.

People that think the book is closed on the subject simply do not fully understand the subject. Which is the same ignorance accusation that armchair scientists throw at the caricature of religious people.

I am not religious at all. However, the above has appeared to me to be blindingly obvious all along, and I've been largely baffled why most (vocal, at least) creationists in particular don't lean this way.

Evolution no more disproves the existence of god than gravity. Both theories can coexist peacefully.

Science is the study of how; religion is the study of why. That's my two bits anyways.

Mandatory flame war starting comment: See its not evolution... its God.

Now discuss...

I like to think it's both.

Why?

Possibly because, from a completely logical perspective, the lack of an irrefutable argument for the existence of God is not proof of non-existence. People are as myopic about evolution disproving God as some Christians (no, not remotely all) are about disproving evolution. Both sides fail to understand the other's arguments and then derive conclusions based on the caricature.

At the very least it disproves the denominations or whatever who proselytize "gospel" which is factually incorrect. It certainly doesn't help God's reputation when it's clear that so many of his follows are witless.

Quote:

It may surprise you to learn that there are Christian churches that teach God as one who works within the laws of the universe instead of vice versa. And such a God is capable of using existing universal forces to organize planets, arrange for life on those planets, and even create a nearly infinite variety of formations in said universe. It may even surprise you further to discover that such a God is not only well within the teachings of the Bible, but has a rather compelling fit with everything we understand about The Way Things Are both scientifically and spiritually.

In any case, attempting to explain away God via evolution is a waste of time since the only thing you can do via evolution is prove that a particular church's teachings are incorrect. And even then, there are undoubtedly further refinements to evolution that will surprise us and may open up possibilities that neither side had considered before.

People that think the book is closed on the subject simply do not fully understand the subject. Which is the same ignorance accusation that armchair scientists throw at the caricature of religious people.

This argument is logically inconsistent because it tries to play both sides to the idea of god of the gaps.

Either God is always going to be in the gaps and therefore largely irrelevant, or he plays in the real world and our hypothesis's are insufficient in a knowable way. Pick one and build a case on it, though I should point out most pick the former out of convenience.

At the very least it disproves the denominations or whatever who proselytize "gospel" which is factually incorrect. It certainly doesn't help God's reputation when it's clear that so many of his follows are witless.

Remember that the followers do not define the leader. That's as much a principle of science (consider the original source material, not the derivative distortions) as it is elsewhere.

tzt wrote:

This argument is logically inconsistent because it tries to play both sides to the idea of god of the gaps.

Either God is always going to be in the gaps and therefore largely irrelevant, or he plays in the real world and our hypothesis's are insufficient in a knowable way. Pick one and build a case on it, though I should point out most pick the former out of convenience.

This is a false dichotomy. Remember that word I used: caricature. You are using your perception of who and what God is to establish that God cannot be both scientific (using the laws of the universe) and spiritual (establishing His own laws or expectations of conduct). This caricatured God cannot play both sides, but also has no relation to reality. Your lack of foundation knowledge does not make my logic inconsistent.

Actually I think the "God of the gaps" notion is flawed. OTOH you can have a God of the laws of physics... which can never be disproved. Ie you can believe in the bible and science/evolution/TV's/radio/the internets etc etc. You just can't believe in a literal interpretation of the bible and whatever you're reading this on .

This is due to the whole the earth is 10,000 years old thing. And Noah's ark and a bunch of other things, basically If the bible is meant to be a literal truth book, then either science is wrong (well our understanding of carbon dating is wrong, as is our understanding of the fossil record, as is our understanding of dinosaurs, as is our understanding of history(stonehenge as is our understanding of DNA, ditto biology etc etc). Or the bible is not the "literal truth".

Actually I think the "God of the gaps" notion is flawed. OTOH you can have a God of the laws of physics... which can never be disproved. Ie you can believe in the bible and science/evolution/TV's/radio/the internets etc etc. You just can't believe in a literal interpretation of the bible and whatever you're reading this on .

This is due to the whole the earth is 10,000 years old thing. And Noah's ark and a bunch of other things, basically If the bible is meant to be a literal truth book, then either science is wrong (well our understanding of carbon dating is wrong, as is our understanding of the fossil record, as is our understanding of dinosaurs, as is our understanding of history(stonehenge as is our understanding of DNA, ditto biology etc etc). Or the bible is not the "literal truth".

Equally flawed, is the idea of the Bible being a book, and that it should be treated as such. The Bible is a collection of books written by several different people across quite a vast period of time. It's not as simple as calling it a work of "fiction" a la "Moby Dick". Do I believe that Adam and Eve frolicked in a garden until Eve ate a doomed fruit? Of course not. Do I believe that Jesus was a man who had a group of followers, and who was charged with sedition against the Roman Empire? Yeah, I do. Did he have some sort of connection with the proposed God of the gaps/physics? I see no reason to discount the possibility. One does not need to take every verse of the Bible "literally" in order to derive more-than-metaphorical meaning in others. When dealing with historical texts of this age, it's damn near impossible to separate fact from fiction. It's a damn shame that so many people are willing to forgo actual thought on the matter, and "authoritatively" proclaim an entire volume --and culture-- to be founded on lies/falsehoods/etc., based solely on the fact that some parts of said volume are likely not factually accurate.

It's been said before, but I'll say it again: Evolution does not disprove the notion of God's existence. Gravity does not disprove the notion of God's existence. The fossil record does not disprove the notion of God's existence. Discovering the Higgs Boson won't... well, you get the point.

Yep no arguments here, nothing in physics is ever going to disprove God (if you go by the God of the laws of physics non-literal bible thing) and i'm also down with your other interpretations of the bible.

My current notion is that Noah's flood was actually the flood of the river-valley civilisations (which we know happened) and the ark, was simply the boat he put his herd animals on. Given how important animal husbandry was back then, having a person (Noah) save his/her animals from the flood would have meant the village/community/their family had animals to help them during the recovery (say breeding stock of of cows, goats, whatever) and possibly saved their lives, and given the import of that time period in our modern times we may not be here if that didn't happen.

At the very least it disproves the denominations or whatever who proselytize "gospel" which is factually incorrect. It certainly doesn't help God's reputation when it's clear that so many of his follows are witless.

Remember that the followers do not define the leader. That's as much a principle of science (consider the original source material, not the derivative distortions) as it is elsewhere.

Ok, so when God went looking for followers, he purposely poison the gospel to either get the most witless motherfuckers out there or at least people who don't mind a leader that lies to them? I don't think this is a road you want to travel further.

Quote:

tzt wrote:

This argument is logically inconsistent because it tries to play both sides to the idea of god of the gaps.

Either God is always going to be in the gaps and therefore largely irrelevant, or he plays in the real world and our hypothesis's are insufficient in a knowable way. Pick one and build a case on it, though I should point out most pick the former out of convenience.

This is a false dichotomy. Remember that word I used: caricature. You are using your perception of who and what God is to establish that God cannot be both scientific (using the laws of the universe) and spiritual (establishing His own laws or expectations of conduct). This caricatured God cannot play both sides, but also has no relation to reality. Your lack of foundation knowledge does not make my logic inconsistent.

Is this knowledge that can be written down in human words or the stuff of yet another gap?

I take it by the thrust of your response that you much favor the confines of the gaps as predicted.

It's been said before, but I'll say it again: Evolution does not disprove the notion of God's existence. Gravity does not disprove the notion of God's existence. The fossil record does not disprove the notion of God's existence. Discovering the Higgs Boson won't... well, you get the point.

The problem with taking the gaps is that god progressively diminishes in importance. Again not a path some are comfortable taking.

#1. So basically the authors are saying that random mutation caused just as many changes as where they thought "sweeps" would occur. So can we conclude that a lot of change in the human genome was random?

#2. So they chose genomes where they "assumed" that there was relative isolation of the subjects and that they had unique evolutionary histories where there was little drift between populations during the past 23,000 years? Bad, bad assumption to make.

#3. Why do you feel the need to start "God flame wars" in these types of threads. Some were taunting people to start the same olde arguments at the beginning. It gets old to keep retreading the same territory.

It is entirely possible humans did not arise from selective pressure at all. Maybe the genes that make us more "us" than other species were not the result of some evolutionary pressure but random. It is possible the change merely put us in a category where we did not have much competition. So the change, which is always random, just put us in a whole new category not more adaptive to certain pressures.

This would help me, at least, to understand why we humans have so many characteristics that don't seem to fit into an "evolutionary advantage" unlike other species. I can understand the ability to have language as an advantage but I see no evolutionary pressure to refine our language skills to the state that they are presently.The same goes for Art, Science, etc. Oh, but having big brains was an evolutionary advantage it has been argued. Really? All I could see evolution giving us is the smarts to be "smart enough". I know this is a subjective thing, what is smart enough? What I see as I look at other species is just being a little smarter is good enough, so why the gift to us, or curse depending on how one views it heh, to be so much smarter?

As I look at modern humans, compared to other species, we are not just given gifts to survive but to really thrive and change the whole nature of the game. What other animal has basically eliminated selective pressures from their species? Humans basically have. Sorry to get all philosophical, but humans have always seemed like they don't really fit the refinement through evolutionary pressure model as well as they should heh.

Your 'mistake' is you only look at inter-species competition, where 'a little smarter' is sufficient to bestow a selective advantage. However, as soon as there is an evolutionary 'arms race', e.g. a snake's poison potency and a prey's resistance, you get a sort of 'runaway trait': the snake having sufficient potency to take down a horse while for it's chosen prey the size of a mouse it's only just enough. The same can happen with intra-species competition, where the bird with the most gaudy plumage gets to mate more often and sire the most offspring, leading to a species of super-gaudy birds. In humans, it's entirely plausible that having to compete in a niche where the only serious competitors are other humans, being smarter than the rest of the species conferred a selective advantage and led to a gradual increase in brain power, eventually encompassing the entire population.

Also, don't mistake survival of the fittest to mean 'being stronger than the rest', or 'better able to survive.' In biology, fitness is measured by the number of an individual's offspring surviving into adulthood, hence an increase in fertility that might even be detrimental to an individual's survival (by taking up more time and resources), could still increase its fitness and thus help propagate said trait throughout the gene pool. In this way saying humans have eliminated selective pressures is only half right. Yes, individuals who in nature would not have survived are now able to do so. Yes, humans are able to adapt to different environment through technical, rather than physical, adaption. But selection is still taking place, but rather in the form of fecundity. Genetic changes that lead to an increased fertility or an increased desire to reproduce are still affecting the number of an individual's offspring, and thus its fitness.

(This'll be my last comment in this thread because it's just not the right place. Feel free to continue elsewhere.)

tzt wrote:

Merovingian wrote:

This is a false dichotomy. Remember that word I used: caricature. You are using your perception of who and what God is to establish that God cannot be both scientific (using the laws of the universe) and spiritual (establishing His own laws or expectations of conduct). This caricatured God cannot play both sides, but also has no relation to reality. Your lack of foundation knowledge does not make my logic inconsistent.

Is this knowledge that can be written down in human words or the stuff of yet another gap?

I take it by the thrust of your response that you much favor the confines of the gaps as predicted.

There are two aspects of "God of the gaps" according to wikipedia (I had to look it up): a) God uses processes not yet understood by science; b) God performs acts that lack plausible natural explanation. While related, they have a subtle difference: (a) presumes that science doesn't know everything (and it doesn't), while (b) implies that we must fit all acts within what science knows.

The problem is that most people come to the table with preconceived notions of a "God of the gaps" wherein God does things like "create" out of nothingness, or violates the laws of physics by existing as an immaterial being (essentially implying "immaterial matter" which is self-contradictory), or exists with a variety of conditions and characteristics that are also self-contradictory. What you need to know is that not all churches teach this kind of God.

On the other hand, any God would still satisfy both (a) and (b), because God's primary act (which few seem to consider) is that he exists. Science cannot explain, and we cannot fit into our known natural laws, an existence of a being that supercedes death and has the capability of organizing our universe. So in that sense (only) would I say that God has to be a God of the gaps to some degree.

On the other hand, God is perfectly capable of abiding by laws of physics that we both have discovered and haven't even begun to discover in order to exist in the way that he does. Are these undiscovered laws supernatural laws? Only in the sense that they exceed our understanding of "natural law". A lot of people have a problem, for example, with Moses parting the Red Sea. It could certainly be myth, but consider the possibility of finding some property of water in the next 20 years that enables us to physically separate a body of water down a particular vector. It's not out of the realm of possibility, but it does not fit within our current understanding of things. I suggest that God could have figured out a way to separate the Red Sea in a manner consistent with all of the properties of water.

I think it takes more than glib remarks to properly discuss God. "God of the gaps" is derogatory to some, but only because both the accuser and the accused do not properly understand (or take the time to think about) the phrase and its implications. I believe in a God that does [edit]not[/edit] fit neatly into today's scientific worldview, but I do believe he knows many many things about laws throughout the universe that we haven't even begun to consider.